An anime-geek friend of mine could probably come up with a whole bunch of Japanese horror stuff, and there are western adult animated films like Felidae, Heavy metal and basically all movies ever created by Ralph Bakshi,
but to me personally, that kind of stuff doesn't really count as particularly messed up since those works were always intended to be dark and weird and aimed at adults (and edgelord teens) who knew what they were watching and presumably old enough to handle it. To me, the most messed up cartoons will always be the ones aimed at children, and some of the worst were made by none other than Disney.
I'm not kidding,
The Black Cauldron was their first attempt at a PG movie and it was full of undead creatures and horrific imagery, and and
one of the deleted scenes, whilst having unfinished animation,
is easily the goriest thing ever animated. I'm not kidding, you really shouldn't open the link at work, unless your workplace is an abattoir.

And then there's
The Hunchback of Notre Dame, which I've already posted on before, but it's just that dark and strange of a movie that I can't resist posting this again;
This is a scene from Schindler's List, a holocaust movie that was rated from age 15 and upwards;
Now compare it against the beginning of
this scene from the hunchback, a movie rated G, deemed fun for the whole family:
Seriously, that story based on a Victor Hugo novel centered on religious persecution, racism and attempted rape was turned into a Disney Musical, with one song featuring
murder and attempted infanticide, a jaunty song where the comedy relief
almost have the heroes lynched, complete with having them placed in gallows with nooses around their necks, and a villain song number literally about
the villain's desire to murder the heroine if he can't force himself on her, all of it
complete with tie-in toys!
But if I may post runner's up, whilst not that scary, it was still weird enough that I spent years thinking this cartoon was just a fever-dream my childhood brain had cooked up:
My Little Pony used to be HEAVY METAL AF.
Also, if you want some vintage lunacy, I can recommend the short film Swing You Sinner's by Max Fleicher (of Betty Boop fame):
So, how do any of these stand against INHUMANOIDS?